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Bacteria are prokaryotic, unicellular organisms. Bacteria are
very small; so much so that 1 billion could fit on 1 square
centimeter of space on the human gums, and 1 gram of digested food
has 10 billion bacteria. Bacteria are the simplest living
organisms. Previously they fell under the Kingdom Moneran, but now
they fall into two different Domains: Archaebacteria and
Eubacteria. There are several differences between the two.
Typically, microbiologists in the 21st century call these groups
"Archaea" and "Bacteria." One of the co-discoverers of the three
Domains has argued that the term "prokaryote" should be removed
from classrooms because it reflects an evolutionary hypothesis that
has been disproved, given that the Archaea are more closely related
to the Eukarya than they are to the Bacteria (Pace 2006,
Nature 441 p. 289).

It is incorrect to think of bacteria as particularly
"simplistic" for all that they do not have internal organelles that
can be visualized using a light microscope. The bacterial nucleoid,
for example, is a highly organized structure even though it
typically contains just one or two circular chromosomes with a
total of millions of basepairs of DNA (Thanbichier et el., 2005,
J Cell. Biochem. 96:506-521; see also http://www.microbelibrary.org/Laboratory%20Diagnostics/details.asp?id=782&Lang=English).
Bacteria have complex cell walls exterior to the cell membrane.
Some bacteria contain plasmids, which are typically circular DNA
with replication that is uncoupled from binary fission (cellular
division). Plasmids in nature often encode traits of significant
interest to humans, such as the ability to be resistant to
clinically important antibiotics, or the ability to degrade "odd"
carbon sources such as TNT or human-made pollutants. Plasmids from
Escherichia coli have been "domesticated" and have long
been in use for genetic engineering, as it is easier to isolate and
modify plasmid DNA, and introduce it into a new cells, than it is
to modify a bacterial chromosome (see "Techniques" at dnai.org; see
also http://www.microbelibrary.org/Laboratory%20Diagnostics/details.asp?id=707&Lang=English).
A few phylogenetic groups of bacteria can make endospores, which
are metabolically inert but are able to resist high temperatures,
radiation, and dessication (see http://www.microbelibrary.org/Laboratory%20Diagnostics/details.asp?id=2511&Lang=English).

Bacterial reproduction is always asexual and usually occurs
through binary fusion, once thought to be a simple process of
growing and dividing. Microbiologists now know, however, that
binary fission is complex in that it requires dozens of proteins
cooperating to build the septum (new cell wall between 'daughter'
cells) and to actively separate the two daughter chromosomes.
Furthermore, there are other forms of reproduction in bacteria, all
of them "asexual" in that they do not use gametes or involve
genetic exchange (Angert 2005, Nature Reviews Microbiology
3:214-224). Genetic exchange in bacteria is instead called
horizontal (or lateral) gene transfer, because bacteria can obtain
genetic information from organisms that are not their parents
(Amabile-Cuevas 2003, American Scientist 91:138-149). (Vertical
genetic transmission is the inheritance of DNA down through the
generations.) Horizontal gene transfer can happen any time and has
nothing to do with cell division. There are three main types,
conjugation which is the sharing of plasmid DNA; transduction,
where a bacterial virus accidentally transfers bacterial DNA from
one bacterium to another, and transformation, where bacteria bind
to DNA in the environment, internalize it, and can use that DNA as
genetic material.

Archaea

Archaea are microbes that are more closely related to Eukaryotic
cells than they are to the Bacteria (http://tolweb.org/tree/home.pages/aboutoverview.html).
Under a light microscope, they visually resemble Bacteria, so that
it wasn't until the advent of the use of molecular methods in
evolutionary biology that they were recognized as belonging to
their own Domain (a phylogenetic grouping above the level of
Kingdom). Archaea have ultrastructural features that are
superficially similar to those in Bacteria but are usually
comprised of distinctive molecules. They do, for example, have a
cell wall, yet that cell wall never contains peptidoglycan.
Instead, peptidoglycan is a unique molecular signature of the
Bacteria. Archaea also have odd lipids in their cell membranes.
They were originally discovered living in extreme environments
thought to resemble conditions on early earth, but now that
microbiologists have become more adept at detecting them, it is
clear that the Archaea are not confined to extreme habitats and can
instead be found everywhere. It is true that some Archaea are
"extremophiles," found in extremely salty or hot environments, but
there are also extremophile Bacteria and even some very unusual
extremophile Eukarya. The best-understood groups of Archaea
are:

Methanogens use Carbon dioxide and Hydrogen to make
Methane. They are found in sewage, cows, and swamps, and they do
not take in oxygen.

Extreme Halophiles live in extremely salty places
(i.e.: the dead sea and great salt lake).

Bacteria

Bacteria have peptidoglycan in their cell walls, and they have
no unusual phospholipids. Bacteria have four shapes:

bacilli (rod shaped)

vibrios (curved shaped)

coccus (round shaped)

spirilli (spiral shaped).

Bacteria can also have prefixes before their names: strepto,
indicating chains of the shaped bacteria, and staphylo, indicating
clusters of the shaped bacteria. A 19th century microbiologist
invented the Gram stain, still used today to differentiate bacteria
into two types, Gram negative and Gram positive (http://en.wikipedia.org/wiki/Hans_Christian_Gram).
These types are not useful in determining phylogeny but can be very
useful in a clinical setting, because Gram negative and Gram
positive bacteria can exhibit differential sensitivity to some
classes of antibiotics. There are probably dozens of "Kingdoms"
within the Domain Bacteria, but the phylogeny of Bacteria is still
disputed as microbiologists continue to study the evolution of
bacteria using molecular methods. Some of the major types of
Bacteria are:

Cyanobacteria are photoautotrophs that strip electrons from
water and use them to fix carbon dioxide; they are a major source
of organic carbon in marine ecosystems.

Spirochetes are Gram negative bacteria that have flexible cells
and internal flagella in an unusual form of a more typical Gram
negative cell wall.

Proteobacteria (E-coli)

Some bacteria produce virulence factors that can cause sickness.
Some examples of these are serotoxins, which are given off by the
Gram positive bacteria, and endotoxins, which are given off by Gram
negative bacteria as they die. There are many other examples,
however, and specific pathogens make a unique suite of virulence
factors that lead to the particular disease caused by that
pathogen.